This is a test version of Biostars. For the public version, visit https://www.biostars.org.
I16 Tag In Vcf File - Samtools Mpileup

Hi, I do not have I16 tag in my VCF file while calling snp using samtools mpileup |bcftools. Does anyone know how to have this tag in INFO field? what options should I use while running the snp call to get this tag in the output?

Thank you very much

-AS

samtools mpileup
• 5,370 views • link
updated by Biostar Biostar • written by aswathyseb • aswathyseb

using "bcftools view" without option outputs I16 values as in:

samtools mpileup -gDSf g1k_v37.fasta file.bam | bcftools view -

but you don't get the I16 if you add arguments to the "bcftools view" (e.g -gcv) , AFAIK.

• 380 views • link
written by sa9 sa9

Thank you very much...:) It was very helpful..

• 0 views • link
written by aswathyseb • aswathyseb

0 answers

No answers yet.

Log in to answer this question.

More posts like this